The villains included a mysterious man named Cain who was hunting Spike for some reason along with Clotho and Atropos.

I only ever drew a few of them, though.

---------------

The Fates are literally the three Fates from Chrono Cross given human form by FATE (just like how Wazuki was turned into Lynx by FATE). Genetic manipulation and all that. They protected Chronopolis from invaders in the game, so their purpose is to protect the FATE computer and, consequentially, the world by preserving the timeline in which Lavos is defeated (the Chrono Compendium calls it the "Ideal Timeline"). Since FATE pretty much created life on El Nido, the three Fates consider themselves the guardians/protectors of the people. So in their own perspectives, they're heroines. Their methods, however, are cold and brutal, so in reality they're far from the pure goddesses they make themselves out to be. They are still computer-created lifeforms with inhuman personalities. At least, Clotho and Atropos are.

Remember, FATE was built from the remainders of Mother Brain, so FATE is considered a "female" AI in my story. FATE considers the Moirae Sisters as her daughters. Atropos is literally Atropos XR from CT, built into the FATE system as Mother Brain and Robo were also assimilated. (As you'll recall, Robo's real name is Prometheus, and the Prometheus Circuit was a part of the FATE computer....)

Clotho is the "leader" of the Moirae Sisters. She is the oldest and existed in 2300 A.D. along with Robo and Atropos XR as part of the R-Series of robots. Calm, cool, and collected, she believes in extreme logic and will do anything, no matter how morally reprehensible, to achieve a satisfactory outcome given her mission directives...as long as it's logical and efficient. She speaks politely and elegantly, and her appearance is the closest one would attribute to a classical "goddess of Fate."

In Chrono Cross, she was the boss "Vita Unus". The Fates' number order does not correspond to their age but rather to their mythological relationship to controlling life and death as the Moriae: Clotho "spun the thread of life" (granted life), Lachesis "measured the length of each thread" (determined lifespan), and Atropos "cut the thread of life" (dealt death).